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Merge branch 'fix/zero-length-single-invariant' (zarr-developers#4334) into fix/mixed-regular-chunk-grid-4374
# Conflicts: # src/zarr/core/metadata/v3.py
2 parents e324baa + 2bf32df commit b2e3c99

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‎.gitattributes‎

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*.py linguist-language=python
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*.ipynb linguist-documentation
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.git_archival.txt export-subst
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# just refuses to format a CRLF file, so `just just-check` would fail on a Windows
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# checkout with core.autocrlf=true before the contributor has changed anything.
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Justfile text eol=lf
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*/justfile text eol=lf
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packages/*/justfile text eol=lf

‎.github/workflows/check_changelogs.yml‎

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- name: Install uv
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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Check zarr-python changelog entries
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run: uv run --no-sync python ci/check_changelog_entries.py
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run: just check-changelogs
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- name: Check zarr-metadata changelog entries
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run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-metadata/changes
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run: just check-changelogs packages/zarr-metadata/changes
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- name: Check zarr-indexing changelog entries
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run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-indexing/changes
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run: just check-changelogs packages/zarr-indexing/changes
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- name: Check zarr-http-server changelog entries
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run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-http-server/changes
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run: just check-changelogs packages/zarr-http-server/changes

‎.github/workflows/codspeed.yml‎

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uses: pypa/hatch@f647ed70d49adb885f53a27d1c7f5bdaeacf2c60
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with:
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version: '1.16.5'
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# No interpreter is set up in this job on purpose. Benchmarks are only comparable
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# across runs if the interpreter underneath them does not move: adding a pinned
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# Python here measured a uniform ~13% slowdown on every benchmark, because hatch
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# then built the environment on that interpreter instead of the runner's own.
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Run the benchmarks
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uses: CodSpeedHQ/action@373d6868929f444bc08d901fd0eb0ad52a8875ea # v5.2.1
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env:
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ZARR_BENCHMARK_CLEAR_CACHE: '1'
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with:
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mode: walltime
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run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed
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run: HATCH_ENV=test.py3.12-minimal just benchmark-codspeed

‎.github/workflows/docs.yml‎

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with:
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persist-credentials: false
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- uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- run: uv sync --group docs
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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# Fast source-level guards that need no built site, so they run before the (slower)
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# build for a quick failure: every public export is in the API reference, and no
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# docstring/Markdown carries reStructuredText markup that MkDocs won't render.
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- run: uv run python ci/check_documented_exports.py docs/api
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- run: uv run python ci/lint_docs.py
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- run: just check-doc-exports
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- run: just lint-docs
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# --strict turns warnings into errors, so a docs code block that fails to execute
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# at build time (e.g. a non-exec python fence disrupting a later exec="true" block)
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# fails CI instead of merging as a silent warning.
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- run: uv run mkdocs build --strict
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- run: just docs-build
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env:
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DISABLE_MKDOCS_2_WARNING: "true"
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NO_MKDOCS_2_WARNING: "true"
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- run: uv run python ci/check_unlinked_types.py
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- run: just check-doc-links
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continue-on-error: true

‎.github/workflows/gpu_test.yml‎

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uses: pypa/hatch@f647ed70d49adb885f53a27d1c7f5bdaeacf2c60
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with:
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version: '1.16.5'
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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# Two names for the same environment on purpose: `just setup` builds whatever
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# HATCH_ENV points at, while `just gpu` reads GPU_HATCH_ENV so that an
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# ambient HATCH_ENV can never redirect `pytest -m gpu` into a CPU environment.
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- name: Set Up Hatch Env
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env:
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HATCH_ENV: gputest.py${{ matrix.python-version }}
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run: |
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hatch env create "$HATCH_ENV"
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hatch env run -e "$HATCH_ENV" list-env
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just setup
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- name: Run Tests
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env:
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HATCH_ENV: gputest.py${{ matrix.python-version }}
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GPU_HATCH_ENV: gputest.py${{ matrix.python-version }}
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run: |
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hatch env run --env "$HATCH_ENV" run-coverage
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just gpu
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- name: Upload coverage
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uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
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uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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flags: gpu

‎.github/workflows/hypothesis.yaml‎

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uses: pypa/hatch@f647ed70d49adb885f53a27d1c7f5bdaeacf2c60
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with:
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version: '1.16.5'
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Set Up Hatch Env
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env:
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HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
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run: |
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hatch env create "$HATCH_ENV"
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hatch env run -e "$HATCH_ENV" list-env
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just setup
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# https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
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- name: Restore cached hypothesis directory
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id: restore-hypothesis-cache
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PYTEST_ADDOPTS: "--report-log=output-${{ matrix.python-version }}-log.jsonl"
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run: |
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echo "Using Hypothesis profile: $HYPOTHESIS_PROFILE"
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hatch env run --env "$HATCH_ENV" run-hypothesis
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just hypothesis
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# explicitly save the cache so it gets updated, also do this even if it fails.
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- name: Save cached hypothesis directory
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key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
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- name: Upload coverage
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uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
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uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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flags: tests

‎.github/workflows/lint.yml‎

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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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with:
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enable-cache: true
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- uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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# `uvx prek` builds each hook's environment from scratch, so cache them the
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# way the prek action used to. Keyed on the hook config: a new pinned rev or
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# a new hook is exactly when the cached environments stop being valid.
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- name: Cache prek hook environments
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uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
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with:
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path: ~/.cache/prek
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# Justfile is hashed too: prek_version lives there, and a bumped prek
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# must not restore a store built by the previous one. No restore-keys
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# fallback for the same reason.
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key: prek-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml', 'Justfile') }}
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- name: Lint
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run: just lint
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- name: Check justfile formatting
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# After the linters, and never masking them: this is cosmetic, and a
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# mis-formatted recipe should not cost someone their ruff/mypy results.
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if: always()
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run: just just-check

‎.github/workflows/test.yml‎

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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- name: Install Hatch
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run: python -m pip install hatch==1.16.5
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Set Up Hatch Env
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env:
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HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
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run: |
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hatch env create "$HATCH_ENV"
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hatch env run -e "$HATCH_ENV" list-env
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just setup
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- name: Run Tests
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HYPOTHESIS_PROFILE: ci
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HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
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run: |
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hatch env run --env "$HATCH_ENV" run-coverage
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just coverage
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- name: Upload coverage
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if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }}
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uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
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uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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flags: tests
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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- name: Install Hatch
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run: python -m pip install hatch==1.16.5
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Set Up Hatch Env
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env:
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HATCH_ENV: ${{ matrix.dependency-set }}
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run: |
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hatch env create "$HATCH_ENV"
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hatch env run -e "$HATCH_ENV" list-env
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just setup
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- name: Run Tests
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env:
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HATCH_ENV: ${{ matrix.dependency-set }}
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run: |
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hatch env run --env "$HATCH_ENV" run-coverage
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just coverage
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- name: Upload coverage
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uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
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uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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flags: tests
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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- name: Install Hatch
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run: python -m pip install hatch==1.16.5
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Set Up Hatch Env
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run: |
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hatch run doctest:pip list
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HATCH_ENV=doctest just setup
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- name: Run Tests
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hatch run doctest:test
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just doctest
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benchmarks:
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name: Benchmark smoke test
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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- name: Install Hatch
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run: python -m pip install hatch==1.16.5
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Run Benchmarks
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env:
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ZARR_BENCHMARK_CLEAR_CACHE: '1'
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run: |
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hatch env run --env "test.py3.13-minimal" run-benchmark
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HATCH_ENV=test.py3.13-minimal just benchmark
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test-complete:
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name: Test complete

‎.github/workflows/zarr-http-server-release.yml‎

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uv run --with "${wheel}" --python 3.12 --no-project \
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python -c "import zarr_http_server; print('zarr_http_server', zarr_http_server.__version__)"
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# The sdist has to stand alone, and `hatch build` above builds the wheel
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# from the source tree, not from the sdist. So build a wheel from the
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# sdist with pip, which unpacks it under the sdist format's rules (no
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# links out of the archive), then run the package's own tests and strict
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# docs build from the unpacked sdist. This job has no checkout, so
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# nothing comes from the repository; zarr, where a package uses it,
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# resolves from PyPI.
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- name: Build a wheel from the sdist with pip
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run: |
76+
sdist=$(ls dist/*.tar.gz)
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uvx --python 3.12 pip@26.2.1 wheel --no-deps --wheel-dir sdist-wheel "${sdist}"
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- name: Install just
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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repo: casey/just
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version: 1.58.0
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- name: Test and build docs from the unpacked sdist
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env:
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UV_PYTHON: '3.12'
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run: |
89+
mkdir sdist
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tar -xzf dist/*.tar.gz -C sdist
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cd sdist/*/
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just test
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just docs-check
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upload_pypi:
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name: Upload to PyPI
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needs: [build, test_artifacts]

‎.github/workflows/zarr-http-server.yml‎

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paths:
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- 'packages/zarr-http-server/**'
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- '.github/workflows/zarr-http-server.yml'
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# The docs config and header script shared by all package sites.
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- 'packages/mkdocs-base.yml'
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- 'packages/source-version.js'
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# The package resolves zarr from the repo root for its own tests, so a
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# core change can break it. Run this suite when core changes too.
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- 'src/zarr/**'
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pull_request:
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paths:
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- 'packages/zarr-http-server/**'
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- '.github/workflows/zarr-http-server.yml'
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# The docs config and header script shared by all package sites.
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- 'packages/mkdocs-base.yml'
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- 'packages/source-version.js'
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# The package resolves zarr from the repo root for its own tests, so a
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# core change can break it. Run this suite when core changes too.
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- 'src/zarr/**'
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- name: Set up Python ${{ matrix.python-version }}
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run: uv python install ${{ matrix.python-version }}
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- name: Install just
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uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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# Pin the tool, not just the action: without this the action
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# installs whatever just is newest at run time.
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just-version: 1.58.0
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repo: casey/just
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version: 1.58.0
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- name: Sync test dependency groups
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# The examples group carries the deps the README examples need, so the
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# test that reads a served array back with a zarr client runs here
@@ -80,11 +85,10 @@ jobs:
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- name: Install uv
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uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
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- name: Install just
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uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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# Pin the tool, not just the action: without this the action
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# installs whatever just is newest at run time.
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just-version: 1.58.0
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repo: casey/just
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version: 1.58.0
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- name: Run ruff
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run: just lint
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- name: Set up Python
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run: uv python install 3.12
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- name: Install just
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uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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# Pin the tool, not just the action: without this the action
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# installs whatever just is newest at run time.
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just-version: 1.58.0
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repo: casey/just
116+
version: 1.58.0
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- name: Sync test dependency group
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run: uv sync --group test --python 3.12
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- name: Run mypy
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with:
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enable-cache: true
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- name: Install just
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uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4
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uses: extractions/setup-crate@7577c1bdf2d95e6d65d532788f35ed79d4b1dda2 # v2.0.1
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with:
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# Pin the tool, not just the action: without this the action
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# installs whatever just is newest at run time.
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just-version: 1.58.0
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repo: casey/just
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version: 1.58.0
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- name: Build docs
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run: just docs-check
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